This paper reports on a study which designed and developed a multi-fingered haptic interface in conjunction with a three-dimensional (3D) virtual model of a section of the cell membrane in order to enable students to work collaboratively to learn cell biology. Furthermore, the study investigated whether the addition of haptic feedback to the 3D virtual reality (VR) simulation affected learning of key concepts in nanoscale cell biology for students aged 12 to 13. The haptic interface was designed so that the haptic feedback could be turned on or switched off. Students (N = 64), in two secondary schools, worked in pairs, on activities designed to support learning of specific difficult concepts. Findings from observation of the activities and interviews revealed that students believed that being immersed in the 3D VR environment and being able to feel structures and movements within the model and work collaboratively assisted their learning. More specifically, the pilot/co-pilot model that we developed was successful for enabling collaborative learning and reducing the isolating effects of immersion with a 3D headset. Results of pre and post-tests of conceptual knowledge showed significant knowledge gains but addition of haptic feedback did not affect the knowledge gains significantly. The study enabled identification of important issues to consider when designing and using haptic-enabled 3D VR environments for collaborative learning.